A technique was developed for the staining of nuclei for DNA using propidium iodide, and incorporated chlorodeoxyuridine (CldUrd) and iododeoxyuridine (IdUrd) using two monoclonal antibodies that showed negligible crossreactivity. The mouse mammary solid tumor MCaK was labeled in vivo by intraperitoneal injection of the nucleosides. Tumor cell nuclei were stained after isolation from ethanol-fixed solid tumor tissue and acid denaturation. The Br3 antibody, which specifically recognizes CldUrd, was applied first, followed by indirect staining with goat anti-mouse phycoerythrin. The direct fluorescein isothiocyanate conjugate of the B44 antibody, which specifically recognizes IdUrd, was then applied. In the direct conjugate form this antibody reacted only minimally with CldUrd. The nuclei were then stained with propidium iodide. With this dye combination the coefficients of variations of the DNA histograms were consistently in the 2-4% range. Two other dye combinations were compared. The propidium iodide/phycoerythrin/fluorescein isothiocyanate dye combination was the simplest because of the compatibility with single laser flow cytometry. Key terms: Propidium iodide, chlorodeoxyuridine, iododeoxyuridine There are several potential applications for the simultaneous and specific quantification of two different halogenated nucleoside analogues in double-labeled DNA. These include direct measurement of recruitment, simultaneous determination of growth fraction and cell kinetics, and more accurate measurement of potential doubling time (T&.A number of bromodeoxyuridine (BrdUrd)-reactive monoclonal antibodies are now commercially available. These antibodies bind differently to the other halogenated thymidine analogues, chlorodeoxyuridine (CldUrd) and iododeoxyuridine (IdUrd). Recently, Bakker et al. (2) described a n indirect method for staining nuclei double-labeled with CldUrd and IdUrd. They found that the monoclonal antibody B44 (5) was minimally reactive to CldUrd after incubation in a highsalt buffer. To stain CldUrd specifically, they used an antibody with minimal reactivity to IdUrd, similar to the Br3 antibody described previously by Vanderlaan et al. (8). Their procedure involved indirect staining of both B44 and the anti-CldUrd-specific antibody. The indirect staining, combined with mandatory incubation and wash in a high-salt buffer, makes the procedure relatively long. Moreover, while Bakker et al. (2) demonstrated simultaneous staining of CldUrd and IdUrd in DNA, they did not show any results of three color flow cytometric analysis.We describe here our investigation of different procedures for three-color analysis of two incorporated halogenated thymidine analogues and DNA. We compared three staining techniques, shortened the staining procedure considerably, and adapted the method for solid tumors labeled in vivo. The simplest method involved the dye combination of phycoerythrin (PE)-tagged second antibody to Br3, fluorescein isothiocyanate (F1TC)-tagged B44, and propidium iodide (PI).